The sanctuary has appealed for help to prevent future flooding, saying it had tried to divert the floodwater but was fighting a losing battle.
Although the waters have receded, director Lyn Friel said the centre would have to wait for drier weather before drainage problems could be tackled.
She told the Belfast Telegraph she would be very keen to get advice from anyone who knows about drainage.
Lyn added that one of the sanctuary’s neighbours pumped out much of the floodwater after it poured down into the centre from the surrounding fields.
“It’s the worst it has been flooded but not the first time it has been flooded,” she said.
Lyn also told how the sanctuary needed every bit of space it could get to house animals, especially since the paddock is unusable as it floods so often.
“The water ran through the back stables and washed away some of our beds,” she added. “A lot of shavings were loose in the beds and the water came through them.
“We also had shavings in bales and they are half-soaked, but we are trying to dry them now.
“Most of our feed was in bins. There were eight bags sitting out that were destroyed.
“Unfortunately, there was dog food that was Christmas presents from people that donated to us — it was sitting on a pallet but it was destroyed.
“The food was worth a few hundred pounds and it’s quite a loss to us.”
Horse rugs donated to the sanctuary were also drenched but can be dried out, Lyn said.
“People have been more than generous over Christmas, and we would love to thank everyone personally,” she added.
“People left feed and horse rugs. A lot of it just appeared like magic. You would have thought the fairies had left it. People need to understand how much we appreciate their generosity – we couldn’t survive without it.”
At the moment, the Crosskennan sanctuary is caring for 58 horses, 28 cats, almost 16 dogs and 20 chickens.
Luckily one horse had just been re-homed, so when floodwater poured into the stables, volunteers were just about able to find space for all the animals to stand.
Among the horses were many welfare cases, some of which were found wandering the roads after being abandoned.
Several years ago, the shelter helped to rescue 15 horses found wandering on Cave Hill in Belfast in deep snow. Lyn is hoping to re-home eight young horses from that group, which are now ready to start their riding careers, as well as many others.
She has appealed to anyone who can help with the sanctuary’s predicament to contact them at 028 9446 5384 and leave a message.
“We were lucky not to lose an awful lot more,” she said.
“We couldn’t manage without people’s generosity — Christmas was overwhelming.”